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Kazuma Aoki was a pilot recruited by G-Force to pilot its first anti-Godzilla weapon, Garuda. However, G-Force scrapped Garuda in favor of the more powerful MechaGodzilla. Kazuma was disappointed that his machine would not see action, but he was recruited to be part of the MechaGodzilla crew. When Kazuma learned that an intact Pteranodon egg had been recovered by Professor Hiroshi Omae, Kazuma traveled to an scientific institute in Kyoto to observe it, since he was a self-proclaimed "pteranodon enthusiast." When Kazuma entered the laboratory, he encountered Azusa Gojo, the scientist placed in charge of watching over the egg. Azusa ordered Kazuma to leave, but not before he managed to steal a small prehistoric fern that had been found with the egg. Kazuma presented the fern to Miki Saegusa, who sensed a strong psychic energy radiating from it. Miki and Kazuma brought the fern to the ESP institute, where the students discovered that it produced a strange melody. The melody was recorded onto a tape and brought to Professor Omae. When the tape was played, the egg at the institute hatched into a baby Godzillasaurus. Azusa called Professor Omae, and he Miki and Kazuma rushed to the laboratory. Fortunately, it was discovered that this baby Godzillasaurus was docile and had imprinted on Azusa as its mother. Azusa named the infant Baby Godzilla and decided to raise him at the institute. Only moments later, Miki detected Godzilla heading directly to Kyoto, likely to retrieve Baby Godzilla. G-Force launched MechaGodzilla, but since Kazuma was in Kyoto they had to use a backup pilot. MechaGodzilla engaged Godzilla in the countryside, but was defeated. As Godzilla drew closer, Kazuma and the others hid Baby Godzilla in the basement of the institute. When Godzilla arrived, he destroyed the institute's upper floors, but could not find the baby. Godzilla finally gave up and returned to the ocean.
When Kazuma returned to G-Force HQ, he told his superior that he was simply using up "a few days' vacation" he had coming. His superior officer responded by demoting him from the MechaGodzilla team and assigning him to parking lot duty. Disgruntled, Kazuma pulled aside Professor Leo Asimov when the latter was trying to leave in his car. Kazuma proposed an idea to increase Garuda's combat power and make it a more viable weapon against Godzilla. Dr. Asimov asked Kazuma what they would do with MechaGodzilla, but Kazuma presented a new plan: combine MechaGodzilla and Garuda to form Super MechaGodzilla. Dr. Asimov approved the idea, and the necessary modifications were made to both mechs. Kazuma visited Azusa at a new holding facility designed specifically for Baby Godzilla. There, he showed her his new robot, pteranodon, which crashed after a short flight demonstration. Later, Miki and the ESP institute's students visited the facility, where the students sang the plant'e melody to Baby Godzilla, which gave him a huge intake of power and caused him to go berserk. Little did they know that the song also revived Rodan and transformed him into Fire Rodan.
G-Force began to implement its final plan to destroy Godzilla, "G-Crusher." Studies had shown that Baby Godzilla had a secondary brain located in his hip that allowed him to move his lower body, suggesting that Godzilla himself possessed a similar structure. Baby Godzilla would be transported to the Ogasawara Islands, luring Godzilla there, where he would be killed by MechaGodzilla. Azusa insisted that she accompany Baby Godzilla as he was carried inside a canister by a helicopter. En route, the helicopter was destroyed by Fire Rodan, who took the canister. MechaGodzilla was launched to battle Rodan, while Kazuma took command of Garuda. Together, MechaGodzilla and Garuda were able to draw Rodan away from the canister, although Garuda was badly damaged. MechaGodzilla used its plasma grenade to blast through Rodan's chest and seemingly kill him. Shortly afterward, Godzilla rose from the sea and battled MechaGodzilla. Kazuma regained consciousness inside the Garuda, and used it to distract Godzilla after MechaGodzilla was knocked down. Finally, MechaGodzilla and Garuda formed Super MechaGodzilla. Using the mech's shock anchor cables, Super MechaGodzilla was able to destroy Godzilla's secondary brain and cripple him. With Godzilla down for the count, Kazuma exited Garuda through his pteranodon robot and landed near the canister, where he asked Azusa if she was okay. Azusa replied that she and Baby were fine, but Baby Godzilla suddenly smashed against the canister doors and broke free, roaring loudly. Rodan heard Baby Godzilla's cries and sacrificed himself to heal Godzilla's brain, allowing him to destroy MechaGodzilla. After the battle, Azusa decided that Baby Godzilla belonged with his own kind, and was forced to leave him behind with Godzilla. Azusa bid farewell to her surrogate son, and left in a helicopter with Kazuma and Professor Omae.
- In one scene, Kazuma meets the ESP institute chief Hosono, who upon learning Kazuma is from G-Force tells him he "doesn't trust him one bit." Hosono is portrayed by actor Tadao Takashima, the father of Kazuma's actor, Masahiro Takashima.